In a report presented to Pakistan’s Supreme Court on Tuesday, the ISI agency alleged President Hamid Karzai’s administration was in league with groups linked to the main Tehrik-e-Taliban Pakistan movement, known collectively as the TTS.

The report suggested the "recent nexus of TTS with Afghan government is likely to enhance the terrorist activities" in areas along the Pakistan-Afghanistan border such as Mohman, Bajaur, Dir, Swat and Chitral.

Jason Reed / Reuters

Secretary of State John Kerry, left, listens to Afghanistan's President Hamid Karzai during their joint news conference at the presidential palace in Kabul on Thursday.

Anti-Pakistan elements, particularly from across the border in Afghanistan, had provided "strong support" in terms of money, logistics and training and this was “one of the main factors for increased militancy,” the report said.

However, it added that the Taliban’s ability to act "at will and to face security forces openly has been substantially curtailed."

The report said that internal rifts within the main Pakistani Taliban group had led to the creation of splinter groups.

"TTS, after having been dislodged from area, has resorted to [suicide bomb and improvised explosive device] attacks" on law-enforcement agencies and other officials, the report said.

The court is considering a case involving seven people who are being kept in one of several internment centers in the border area, despite being acquitted by an anti-terrorism court because of lack of evidence against them.

The ISI report was submitted to justify the internment centers and military operations against militants more generally.

The ISI said it was not going to release people held at the internment centers, warning that the detainees included terrorists who could go to cities like Islamabad and Lahore and launch attacks.

It said that 3,871 Pakistani security personnel, more than 3,000 militants and more than 5,000 civilians had been killed in the border area in the last five years.

There had been 235 suicide attacks, 9,257 rocket attacks and 4,256 bombings during the same period, the report added.

Afghanistan and Pakistan have a difficult relationship.

Islamabad has accused Kabul of failing to stop anti-government militants from operating from mountain havens in Afghanistan, while Kabul has blamed Pakistan’s military for cross-border shelling.

U.S. Secretary of Defense Chuck Hagel responds to Afghan President Hamid Karzai's statements in which Karzai accused the U.S. and Taliban with working together.

In September, Afghanistan’s foreign minister told the United Nations Security Council that diplomatic ties with Pakistan were under threat.

On Monday, after a private meeting with Secretary of State John Kerry in Kabul, Karzai insisted he had not meant to suggest that the United States was colluding with the Taliban, Reuters reported.

"I never used the word 'collusion' between the Taliban and the U.S. Those were not my words. Those were the [words] picked up by the media," he said.

Kerry said the two men had discussed the matter but he played it down, Reuters reported. "I am confident that the president absolutely does not believe that the United States has any interest except to see the Taliban come to the table to make peace."